6LFM

Cryo-EM structure of a class A GPCR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of CXC chemokine receptor 2 activation and signalling.

Liu, K.Wu, L.Yuan, S.Wu, M.Xu, Y.Sun, Q.Li, S.Zhao, S.Hua, T.Liu, Z.J.

(2020) Nature 585: 135-140

  • DOI: 10.1038/s41586-020-2492-5
  • Primary Citation of Related Structures:  
    6LFM, 6LFL, 6LFO

  • PubMed Abstract: 
  • Chemokines and their receptors mediate cell migration, which influences multiple fundamental biological processes and disease conditions such as inflammation and cancer 1 . Although ample effort has been invested into the structural investigation of the chemokine receptors and receptor-chemokine recognition 2-4 , less is known about endogenous chemokine-induced receptor activation and G-protein coupling ...

    Chemokines and their receptors mediate cell migration, which influences multiple fundamental biological processes and disease conditions such as inflammation and cancer 1 . Although ample effort has been invested into the structural investigation of the chemokine receptors and receptor-chemokine recognition 2-4 , less is known about endogenous chemokine-induced receptor activation and G-protein coupling. Here we present the cryo-electron microscopy structures of interleukin-8 (IL-8, also known as CXCL8)-activated human CXC chemokine receptor 2 (CXCR2) in complex with G i  protein, along with a crystal structure of CXCR2 bound to a designed allosteric antagonist. Our results reveal a unique shallow mode of binding between CXCL8 and CXCR2, and also show the interactions between CXCR2 and G i  protein. Further structural analysis of the inactive and active states of CXCR2 reveals a distinct activation process and the competitive small-molecule antagonism of chemokine receptors. In addition, our results provide insights into how a G-protein-coupled receptor is activated by an endogenous protein molecule, which will assist in the rational development of therapeutics that target the chemokine system for better pharmacological profiles.


    Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai, China. liuzhj@shanghaitech.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A353Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B346Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-8D, E72Homo sapiensMutation(s): 0 
Gene Names: CXCL8IL8
Membrane Entity: Yes 
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Find proteins for P10145 (Homo sapiens)
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PHAROS:  P10145
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 2F [auth R]360Homo sapiensMutation(s): 0 
Gene Names: CXCR2IL8RB
Membrane Entity: Yes 
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Find proteins for P25025 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
scFv16G [auth S]259Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
H [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references